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Ferreira P.,University of Évora | Fonseca I.M.,REQUIMTE | Ramos A.M.,REQUIMTE | Vital J.,REQUIMTE | Castanheiro J.E.,University of Évora
Applied Catalysis B: Environmental | Year: 2010

The acetalisation of glycerol was studied using heteropolyacids, immobilized in silica, as catalysts, at 70 °C. The main product of glycerol acetalisation was solketal. The tungstophosphoric (PW), molybdophosphoric (PMo), tungstosilisic (SiW) and molybdosilisic (SiMo) acids were immobilized in silica by sol-gel method. It was observed that the catalytic activity decreases in the series: PW_S > SiW_S > PMo_S > SiMo_S. All catalysts exhibited good values of selectivity to solketal (about 98% near complete conversion). The effect of different parameters, such as catalyst loading, molar ratio of glycerol to acetone and temperature on the glycerol acetalisation, over PW_S catalyst, was studied. Catalytic stability of the PW_S, SiW_S, PMo_S and SiMo_S catalysts was evaluated by performing consecutive batch runs with the same catalyst sample. After the third batch, it was observed a stabilisation of the initial activity. © 2010 Elsevier B.V. All rights reserved.

Carvalho A.T.P.,Requimte | Fernandes P.A.,Requimte | Ramos M.J.,Requimte
Journal of Chemical Theory and Computation | Year: 2011

Eukaryotic RNA polymerase II (RNAP II) transcribes the DNA into mRNA. The presence of two metal ions (usually Mg 2+) and conserved aspartate residues in the active sites of all nucleic acid polymerases led to the adoption of a universal catalytic mechanism, known as the "two metal ion catalysis". In this scheme, it is assumed that the coordination shell of Mg 2+ (geometry, number, and identity of the ligands) is basically the same for all of the enzymes, despite the significant differences in sequence and structure commonly found in multisubunit RNA polymerases versus single-subunit RNA polymerases and DNA polymerases. Here, we have studied the catalytic mechanism of RNAP II and found very interesting variations to the postulated mechanism. We have used an array of techniques that included thermodynamic integration free energy calculations and electronic structure calculations with pure DFT as well as hybrid DFT/semiempirical methods to understand this important mechanism. We have studied four different catalytic pathways in total, resulting from different combinations of proton donors/acceptors for the two proton transfers experimentally detected (deprotonation of the 3′ hydroxyl of the terminal nucleotide (HO RNA) and protonation of pyrophosphate). The obtained data unambiguously show that the catalytic mechanism involves the deprotonation of HO RNA by a hydroxide ion coming from the bulk solvent, the protonation of pyrophosphate by the active site His1085, and the nucleophilic attack to the substrate by O - RNA. The overall barrier is 9.9 kcal/mol. This mechanism differs from those proposed in the identity of the general acid. The deprotonation of the HO RNA and the transition state for the nucleophilic attack are similar to some (but not all) of the family members. © 2011 American Chemical Society.

Moreira I.S.,REQUIMTE | Fernandes P.A.,REQUIMTE | Ramos M.J.,REQUIMTE
Journal of Computational Chemistry | Year: 2010

Protein-protein binding is one of the critical events in biology, and knowledge of proteic complexes three-dimensional, structures is of fundamental importance for the biochemical study of pharmacologic compounds. In the past two decades there was an emergence of a large variety of algorithms designed, to predict the structures of protein-protein complexes-a procedure named docking. Computational methods, if accurate and reliable, could play an important role, both to infer functional properties and to guide new experiments. Despite the outstanding progress of the methodologies developed in this area, a few problems still prevent protein-protein docking to be a widespread practice in the structural study of proteins. In this review we focus our attention on the principles that govern docking, namely the algorithms used for searching and scoring, which are usually referred as the docking problem. We also focus our attention on the use of a flexible description of the proteins under study and the use of biological information as the localization of the hot spots, the important residues for protein-protein binding. The most common docking softwares are described too. © 2009 Wiley Periodicals, Inc.

Teixeira V.,CIQ UP | Feio M.J.,REQUIMTE | Bastos M.,CIQ UP
Progress in Lipid Research | Year: 2012

Antimicrobial peptides (AMPs) take part in the immune system by mounting a first line of defense against pathogens. Recurrent structural and functional aspects are observed among peptides from different sources, particularly the net cationicity and amphipathicity. However, the membrane seems to be the key determinant of their action, either as the main target of the peptide action or by forming a barrier that must be crossed by peptides to target core metabolic pathways. More importantly, the specificity exhibited by antimicrobial peptides relies on the different lipid composition between pathogen and host cells, likely contributing to their spectrum of activity. Several mechanisms of action have been reported, which may involve membrane permeabilization through the formation of pores, membrane thinning or micellization in a detergent-like way. AMPs may also target intracellular components, such as DNA, enzymes and even organelles. More recently, these peptides have been shown to produce membrane perturbation by formation of specific lipid-peptide domains, lateral phase segregation of zwitterionic from anionic phospholipids and even the formation of non-lamellar lipid phases. To countermeasure their activity, some pathogens were successful in developing effective mechanisms of resistance to decrease their susceptibility to AMPs. The functional and integral knowledge of such interactions and the clarification of the complex interplay between molecular determinants of peptides, the pathogen versus host cells dichotomy and the specific microenvironment in which all these elements convene will contribute to an understanding of some elusive aspects of their action and to rationally design novel therapeutic agents to overcome the current antibiotic resistance issue. © 2012 Elsevier Ltd. All rights reserved.

Alves V.D.,REQUIMTE | Costa N.,REQUIMTE | Coelhoso I.M.,REQUIMTE
Carbohydrate Polymers | Year: 2010

In this work, the enhancement of the barrier properties to water vapour and gases (CO2 and O2) of a polymeric matrix composed by kappa-carrageenan and pectin (66.7% kappa-carrageenan), with the inclusion of mica flakes, was studied. The effect of the films mica content on the water vapour permeability (WVP) was dependent on the driving force applied. A higher WVP reduction (of about 40% for a mica content of 10%, mass of mica per mass of dry polymer), was observed when the films were more homogenously hydrated throughout their thickness. A significant decrease was also observed for both CO2 and O2 permeabilities (73% and 27%, respectively), in conditions where the films were plasticized with water (25% of water, dry basis), for which there is a depletion of the good barrier properties characteristic of dry polysaccharide films. In addition, the composition of 10% of mica flakes in the polymer matrix represented a critical volume fraction of inorganic particles, above which there was a decrease of the films barrier properties, for all components tested. © 2009 Elsevier Ltd. All rights reserved.

Reis T.C.,REQUIMTE | Correia I.J.,University of Beira Interior | Aguiar-Ricardo A.,REQUIMTE
Nanoscale | Year: 2013

The rational design of three-dimensional electrospun constructs (3DECs) can lead to striking topographies and tailored shapes of electrospun materials. This new generation of materials is suppressing some of the current limitations of the usual 2D non-woven electrospun fiber mats, such as small pore sizes or only flat shaped constructs. Herein, we pursued an explanation for the self-assembly of 3DECs based on electrodynamic simulations and experimental validation. We concluded that the self-assembly process is driven by the establishment of attractive electrostatic forces between the positively charged aerial fibers and the already collected ones, which tend to acquire a negatively charged network oriented towards the nozzle. The in situ polarization degree is strengthened by higher amounts of clustered fibers, and therefore the initial high density fibrous regions are the preliminary motifs for the self-assembly mechanism. As such regions increase their in situ polarization electrostatic repulsive forces will appear, favoring a competitive growth of these self-assembled fibrous clusters. Highly polarized regions will evidence higher distances between consecutive micro-assembled fibers (MAFs). Different processing parameters-deposition time, electric field intensity, concentration of polymer solution, environmental temperature and relative humidity-were evaluated in an attempt to control material's design. © 2013 The Royal Society of Chemistry.

Gawande M.B.,REQUIMTE | Pandey R.K.,Marquette University | Jayaram R.V.,Institute of Chemical Technology
Catalysis Science and Technology | Year: 2012

A variety of mixed metal oxides (MMOs), containing alkali, alkaline, rare earth and noble metals, and their applications are presented. In this mini review, we summarize versatile applications of mixed metal oxides in organic synthesis. A variety of reactions such as reduction, oxidation, multicomponent, Mannich, alkylation, condensation, deprotection, cycloaddition, hydroxylation, dehydration, dehydrogenation, transesterification, reactions involving biomimetic oxygen-evolving catalysts and other important C-C bond forming reactions are well presented on the surface of mixed metal oxides under a variety of reaction conditions. The scope of MMOs in important organic reactions, industrial applications, and green chemistry and recent applications of MMOs are well presented in this review. © 2012 oyal Society of Chemistry.

Bonifacio V.D.B.,REQUIMTE
Journal of Chemical Education | Year: 2012

A quick response coded audio periodic table of the elements (QR-APTE) was developed using free online resources. The potential of QR-APTE was tested using a smart phone and is envisaged to become a truly powerful tool to teach chemistry to blind and visually impaired students under a mobile-learning environment. © 2012 American Chemical Society and Division of Chemical Education, Inc.

Assuncao M.,University of Porto | Santos-Marques M.J.,University of Porto | Carvalho F.,REQUIMTE | Andrade J.P.,University of Porto
Free Radical Biology and Medicine | Year: 2010

We previously found that prolonged consumption of green tea (GT), a rich source of antioxidant polyphenols, protected proteins and lipids against oxidation and reduced lipofuscin deposition in the rat hippocampal formation as well as improving spatial memory during aging. In this work, we sought to investigate whether GT treatment could interfere with age-related changes in redox status and cellular signaling systems related to oxidative stress and survival in the same brain region. To address this issue, five male Wistar rats were fed with GT from 12 to 19 months of age and results were compared to those obtained from controls age 19 months (C-19 M). A third group of rats was evaluated at 12 months of age to provide baseline data. At completion of the specified time points, the glutathione levels and antioxidant enzyme activities, the activation of the transcription factors cyclic AMP response element-binding (CREB) and nuclear factor-κB (NF-κB, p50 and p65 subunits), and the levels of brain-derived neurotrophic factor (BDNF) and B-cell lymphoma-2 (Bcl-2) were measured in hippocampal formations. GT-treated rats presented higher reduced and lower oxidized glutathione levels and displayed favorable alterations in antioxidant enzyme activities compared to C-19 M animals. In addition, GT increased CREB activation and the levels of BDNF and Bcl-2, but had no effect on activation of NF-κB subunits, relative to age-matched controls. We conclude that long-term GT ingestion improves antioxidant systems and activates CREB in the aging rat hippocampal formation, leading to neuroprotection mediated by downstream upregulation of BDNF and Bcl-2. © 2010 Elsevier Inc. All rights reserved.

Chemical Communications | Year: 2011

Ionic liquids can be made intrinsically electrochromic and magnetic through the appropriate combination of electrochromic and magnetic anions based on ethylenediaminetetraacetic metal complexes, combined with several organic cations. These novel and highly multi-functional materials encompass the peculiar properties of ionic liquids together with the characteristics of electrochromic and magnetic materials. © 2011 The Royal Society of Chemistry.

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